Word and Excel mostly.
I've created a simple Word template for the current format for monsters as used in Dungeon and MM 4. I tend to use it to create individual pages for the opponents my party will face. Once saved as a template I create a new page for a creature from the File -> New... option in Word. I've found that taking the time to type out the stats for the baddies helps a lot in knowing their abilities, planning tactics, and also makes it wicked easy to keep track of them during combat, since I don't have to flip through books or magazines.
Excel I use to create an area-by-area list of creatures, their hit points, and any notable special abilities such as fast healing or damage reduction. I make one entry for each creature, and then print this out and use it to track hit points in combat.
I know none of this is earth-shatteringly amazing, but what I have found amazing is how much more organized I am now running my games with these simple changes. I'll try to attach my Word template for anyone interested. I can only attach it as a document, so if you download it, open it in Word and then use File->Save As... to save it as a template (.dot).